Phylogenomics reveal species limits and inter-relationships in the narrow-range endemic lycian salamanders

• Published in: Molecular phylogenetics and evolution p. 108205
• Main Authors: Scott, Peter A., Najafi-Majd, Elnaz, Yıldırım Caynak, Elif, Gidiş, Müge, Kaya, Uğur, Bradley Shaffer, H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09.10.2024
• Subjects: Bayesian species delimitation; ddRADseq; L. finikensis comb. nov; Lyciasalamandra; Bayesian species delimitation; Lyciasalamandra; L. finikensis comb. nov; ddRADseq
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108205

[Display omitted] •Salamanders of the genus Lyciasalamandra were sampled comprehensively throughout Mediterranean coast of Turkey and a handful of Aegean Islands.•DdRADseq was used to generate > 220,000 SNPs from > 110,000 RAD-loci for 110 specimens of Lyciasalamandra.•Multiple methods of lineage discovery were used to infer putative operational taxonomic units in the genus.•Multiple Bayesian species delimitation methods are used to infer species limits and infer interspecific relationships for the genus and a new taxonomy is provided. Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.